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Richard Griffin, 64, William Hammersley, 79, and Harry Cadman, 71, died in the summer of 2012 while many others were affected.
A hot tub on display at the JTF warehouse in Stoke-on-Trent was the "probable source" of the outbreak, the Health Protection Agency said.
JTF declined to comment on the settlement.
Mr Griffin's daughter, Rachel, who now lives in Cumbria, said she was relieved compensation had been agreed without the need for a court battle.
"Nothing can ever bring our dad back but we just wanted to make sure that justice was done and that there was some accountability for his death," she said.
"I truly hope no-one ever has to go through what we have."
The outbreak struck more than 20 people in the summer of 2012.
Mr Griffin contracted the disease while delivering meat to a café in the JTF Warehouse.
He initially suffered headaches and hallucinations and later lost consciousness at his home in Clayton. He died in hospital from multiple organ failure.
The Health Protection Agency confirmed the hot tub on display at the JTF Warehouse, off King Street in Fenton, contained the same strain of Legionella as those who had become ill.
Inquests are set to take place next year and the Crown Prosecution Service has not yet decided whether to pursue charges.
Irwin Mitchell, which has been representing affected families, said JTF had admitted civil liability.
"Nothing can turn back the clock but we are pleased to have finally concluded these cases, allowing those families affected to begin to move on with their lives," said lawyer Amandeep Dhillon.
More than £200,000 has been awarded to families after a fatal outbreak of Legionnaires' disease.